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As a die-hard Emacs user, I think that org-mode with it's org-babel capabilities blows Jupyter out of the water, and it produces much better, readable output. Y

As a die-hard Emacs user, I think that org-mode with it's org-babel capabilities blows Jupyter out of the water, and it produces much better, readable output. You can use it with pretty much any language, and combine several languages in a single document without any issues. Besides all this, it's just a plain text format, and you can extract all the code into proper source files for later offline use, too ('tangling', in literate programming parlance). Jupyter uses a rather obtuse json format which is not practical to work on directly. Of course, it's not web-based and it requires some basic knowledge of Emacs, but functionality-wise is so much better that it ends up being frustrating to use Jupyter when collaborating with other people. There are some workarounds (EIN, and ob-ipython modes help, but it's not quite the same)

emj 9y ago
Requiring basic Emacs knowledge is just too much, just looking through the features of org-babel I can't really find anything that makes it better suited. Except not having to bother with a webbrowser, that is a nice plus, but hardly important for most people I work with.
- abhirag 9y ago
  I have used both Jupyter Notebooks and org mode with org-babel extensively and I agree with the OP regrading the fact that the org-babel workflow is vastly superior, OP did point out a few features which org mode workflow has and Jupyter Notebooks don't but I will try and provide a comprehensive list: 1. Plain text format, git and git diffs work 2. You can combine many languages in a single document, and every code block can be part of a separate session, as an analogy to Jupyter Notebooks, you can have multiple kernels backing a single notebook and you can decide what kernel you want the current code block to run in. 3. You can edit a code block in the major mode for that language, i.e. you get all the features of Emacs while editing code: documentation, auto-complete, snippets and anything Emacs can do, and Emacs can do a lot :) 4. You can have internal and external links to any part of the document (or any other org-mode file) within the editor which get exported as links in the HTML file too. Want to refer to a code block you used before, just name it and drop a link. Extremely useful in binding the whole document together. 5. Literate Programming support -- You can decide the order the concepts are introduced in according to the human reader, not according to the execution order the machine demands it to be in: #+NAME: named_code_block :eval no function_not_defined_yet() #NAME: complete_code_block def function_not_defined_yet(): print("nice function innit?") <<named_code_block>> The <<named_code_block>> gets expanded to whatever you defined it and you control the way you want to structure the document to be the most readable. You can keep working backed by a REPL in the initial stages and then extract(tangle in literate programming speak) to a file, again in the order you want using the <<named_code_block>> (NOWEB syntax). So one org-mode can generate your whole project if you wish so. 6. With the internal and external links and <<named_code_block>> (NOWEB syntax) the org-mode file is closer to being a hypertext file than Jupyter Notebook even though Jupyter Notebook is the one running in a browser. I have covered only the major features of org-babel, I haven't even covered all the features. I love Jupyter Notebooks too, but org-babel is something else. I am currently working on a toy ray tracer in Clojure in literate programming style and loving every moment :)
  - tincholio 9y ago
    You saved me a whole lot of typing! Thanks :) I'd add that you can also benefit from other aspects of org, such as project management functionality, outline editing, table editing, tables with formulas, direct git integration via Magit, etc., etc. I agree that getting people on Emacs is a non-minor issue, but using something like Spacemacs with CUA-mode enabled could go a long way towards acceptance.
    - abhirag 9y ago
      I would love discussing the literate ray tracer I have been working on and the literate programming workflow I have made for it. Couldn't find your email in the profile, mine is abhirag@outlook.com, would be great to discuss if I can improve my workflow further :)
      - tincholio 9y ago
        Just sent you a mail (check spam folder if you don't see it, it comes from my own domain, and sometimes it's dumped with the spam)
        abhirag 9y ago
        Found it in the spam folder, will mail you the details soon :)
  - emj 9y ago
    I will try to run a org-mode to ipynb converter, so thanks to your suggestion! I just wish there was an Emacs version that wasn't to differnt from everything else so other people could look past the stigma of Emacs. So thank you for the feature run down, and to be cyrstal clear I want more options, but I will only be able to run org-mode/babel myself. Requiring Emacs is just too big of an hurdle for anything bigger than a two man team.
    - abhirag 9y ago
gaius 9y ago
combine several languages in a single document without any issues You can do this with RMarkdown as well, despite the name, and run notebooks in RStudio. Much better experience than Jupyter in a browser. https://yihui.name/knitr/demo/engines/ https://yihui.name/knitr/demo/engines/
- tincholio 9y ago
  I haven't used Knitr (I do my R stuff from within Emacs, and org is a natural choice there), but it does look pretty powerful
- _Wintermute 9y ago
  RMarkdown is pretty useless if you're not using R. Except engine='R' (default), all chunks are executed in separate sessions, so the variables cannot be directly shared. So yes you can write a python snippet, but good luck trying to write a notebook.
dahart 9y ago
> org-babel capabilities blows Jupyter out of the water ... Besides all this, it's just a plain text format This feels like the argument against Slack in favor of IRC. I don't doubt it's true for you that org-babel is better, but there isn't really even that much comparison between Jupyter and org-babel, they are very different things. One of the more compelling reasons to use Jupyter is inline images and plots. Another one of the more compelling reasons to use it is it basically comes bundled with everything you need, python with it's own virtual environment that doesn't modify your system python, and a bunch of amazing libraries, numpy, scipy, matplotlib. Not needing to know emacs helps too, but that's really low on the list. > Jupyter uses a rather obtuse js on format which is not practical to work on directly. This is a wierd thing to say. Jupyter has download as .py right in the file menu. Not to mention download as Markdown, HTML, LaTeX or PDF, if you want to present or share instead of export the python.
- tincholio 9y ago
  > One of the more compelling reasons to use Jupyter is inline images and plots You can do those in org, since forever. I meant that the files themselves are plain text, which is good for sharing, version control, etc. ipynb files embed images with Base64 encoding, which makes seeing diffs a major PITA. >This is a wierd thing to say. Jupyter has download as .py right in the file menu. Not to mention download as Markdown, HTML, LaTeX or PDF, if you want to present or share instead of export the python. You can export org to those formats and more, but the main part is that you can organize your code (e.g, tangling to different files, etc.), and use other languages than python (or whatever other kernel you're running in Jupyter). Plus, you get to use a proper text editor instead of editing on a browser textarea.
  - dahart 9y ago
    I Agree with all those points. I've used org mode for a few things, but not for python notebooks. I remember seeing a great video a few years back on using python in org mode to make a research notebook. It really made me want to try org mode for literate / notebook style programming. I think it was this one: https://youtu.be/1-dUkyn_fZA https://youtu.be/1-dUkyn_fZA It sounds like org mode does not store images inline, since you don't like the b64 images in Jupyter? I imagine that could go both ways depending on what you want. Even for diffing, you might like to see that the image changed (though I generally agree that diffing images is not ideal). If you have to package images separately when sharing, then wouldn't inline images score a point for easier sharing? > use other languages that python Agreed, and that is powerful, but this also goes to my point. Jupyter is made for python and org mode isn't. Jupyter comes with python and libraries, where with Emacs you're on your own to figure out how to install and use different languages, and setup your environment so Emacs can see them. You're on your own to bring in images and plots, where Jupyter already understands commands that output images. > Plus, you get to use a proper text editor instead of editing on a browser textarea. Yes, but the editor is Emacs. :) For a lot of people the browser textarea is a bonus because it's the same thing you use everywhere. It's uncomplicated and non-technical and utterly consistent, even if lacking any power.
todd8 9y ago
I share your opinion about the superiority of org-mode as a means to assemble a document out of various pieces. It's not hard to show nicely formatted code, the code's output, the math behind the code and perhaps a graph of the results all in a LaTeX/PDF document and or HTML. All of this can be done with a flat text file that is easy to save as a part of a project under source control. What I wonder is why are Jupyter notebooks so popular? I've tried them, but perhaps I don't understand the workflow in the way people use them. Are they intended to be works in progress where one explores ideas and looks at results? This is how I've usually used them and Mathematica's notebooks as well. For me though, my Jupyter or Mathematica notebooks end up with lots of false steps and dead-ends. To prepare a presentable form of the results I have to go back and edit the notebook to such a degree that it doesn't feel like working in a notebook as much as it is working in a complex document with a really weak set of editing tools. To be fair, I haven't used Jupyter or Mathematica for a couple of years and things may have changed. Maybe HN readers can help be understand how to more effectively use these tools.
- tincholio 9y ago
  > What I wonder is why are Jupyter notebooks so popular? I often wonder the same. I'm now kinda forced to use them, since they're the tool of choice in my team, but it's a major pain. I think that they're "easy" (in the way Rich Hickey describes "easy" vs "simple") to get started with (just as python, btw), but their lack of flexibility comes back to bite you sooner or later. For me, I've resorted to using a mix of EIN and ob-ipython, and then copy/pasting as needed to keep the stuff in synch with Jupyter. I'm now considering writing a simple ox-jupyter exporter, and maybe some import functionality, to avoid dealing with Jupyter directly. John Kitchin has written a basic exporter (http://kitchingroup.cheme.cmu.edu/blog/2017/01/21/Exporting-org-mode-to-Jupyter-notebooks/ http://kitchingroup.cheme.cmu.edu/blog/2017/01/21/Exporting-...), but it doesn't support inline images (it should be simple to fix this), and it doesn't really adhere to the ox- style of exports, so I think I'll probably do my own instead of adapting his (it'll be a good learning experience, for sure).
- dahart 9y ago
  > What I wonder is why are Jupyter notebooks so popular? How easy is it to share a Jupyter notebook with someone else, versus sharing an org-mode notebook? Think about the recipients rather than how hard it is for you. Assume the person you share with needs to be able to re-run your notebook. Assume the person you share with isn't using the same operating system that you are. Be honest and think about all the steps involved. With Jupyter, I send a single install link to Anaconda. With Emacs + org mode + python + numpy + scipy + matplotlib, I might not even know where to begin if the recipient is using Windows or Mac. The recipient needs to install emacs, and they need to know how to use Emacs. They have to know how to install python packages (and possibly a package manager), and ideally be able to use virtualenv too. If I need different libraries than what Anaconda comes with, I can put the commands in the notebook, and I won't mess up the recipient's system version of Python. With org-mode, they'd need to figure it out on their own. If I choose to use a different language than Python in my org-node notebook, the recipient will have to install that programming language and environment themselves before they can use your notebook. It's the simplicity and bundling of dependencies that make Jupyter popular. All the flexibility and power you get with org mode comes at a high price.

emj 9y ago

Requiring basic Emacs knowledge is just too much, just looking through the features of org-babel I can't really find anything that makes it better suited. Except not having to bother with a webbrowser, that is a nice plus, but hardly important for most people I work with.

abhirag 9y ago
I have used both Jupyter Notebooks and org mode with org-babel extensively and I agree with the OP regrading the fact that the org-babel workflow is vastly superior, OP did point out a few features which org mode workflow has and Jupyter Notebooks don't but I will try and provide a comprehensive list: 1. Plain text format, git and git diffs work 2. You can combine many languages in a single document, and every code block can be part of a separate session, as an analogy to Jupyter Notebooks, you can have multiple kernels backing a single notebook and you can decide what kernel you want the current code block to run in. 3. You can edit a code block in the major mode for that language, i.e. you get all the features of Emacs while editing code: documentation, auto-complete, snippets and anything Emacs can do, and Emacs can do a lot :) 4. You can have internal and external links to any part of the document (or any other org-mode file) within the editor which get exported as links in the HTML file too. Want to refer to a code block you used before, just name it and drop a link. Extremely useful in binding the whole document together. 5. Literate Programming support -- You can decide the order the concepts are introduced in according to the human reader, not according to the execution order the machine demands it to be in: #+NAME: named_code_block :eval no function_not_defined_yet() #NAME: complete_code_block def function_not_defined_yet(): print("nice function innit?") <<named_code_block>> The <<named_code_block>> gets expanded to whatever you defined it and you control the way you want to structure the document to be the most readable. You can keep working backed by a REPL in the initial stages and then extract(tangle in literate programming speak) to a file, again in the order you want using the <<named_code_block>> (NOWEB syntax). So one org-mode can generate your whole project if you wish so. 6. With the internal and external links and <<named_code_block>> (NOWEB syntax) the org-mode file is closer to being a hypertext file than Jupyter Notebook even though Jupyter Notebook is the one running in a browser. I have covered only the major features of org-babel, I haven't even covered all the features. I love Jupyter Notebooks too, but org-babel is something else. I am currently working on a toy ray tracer in Clojure in literate programming style and loving every moment :)
- tincholio 9y ago
  You saved me a whole lot of typing! Thanks :) I'd add that you can also benefit from other aspects of org, such as project management functionality, outline editing, table editing, tables with formulas, direct git integration via Magit, etc., etc. I agree that getting people on Emacs is a non-minor issue, but using something like Spacemacs with CUA-mode enabled could go a long way towards acceptance.
  - abhirag 9y ago
    I would love discussing the literate ray tracer I have been working on and the literate programming workflow I have made for it. Couldn't find your email in the profile, mine is abhirag@outlook.com, would be great to discuss if I can improve my workflow further :)
    - tincholio 9y ago
      Just sent you a mail (check spam folder if you don't see it, it comes from my own domain, and sometimes it's dumped with the spam)
      - abhirag 9y ago
        Found it in the spam folder, will mail you the details soon :)
- emj 9y ago
  I will try to run a org-mode to ipynb converter, so thanks to your suggestion! I just wish there was an Emacs version that wasn't to differnt from everything else so other people could look past the stigma of Emacs. So thank you for the feature run down, and to be cyrstal clear I want more options, but I will only be able to run org-mode/babel myself. Requiring Emacs is just too big of an hurdle for anything bigger than a two man team.
  - abhirag 9y ago

gaius 9y ago

combine several languages in a single document without any issues You can do this with RMarkdown as well, despite the name, and run notebooks in RStudio. Much better experience than Jupyter in a browser. https://yihui.name/knitr/demo/engines/ https://yihui.name/knitr/demo/engines/

tincholio 9y ago
I haven't used Knitr (I do my R stuff from within Emacs, and org is a natural choice there), but it does look pretty powerful
_Wintermute 9y ago
RMarkdown is pretty useless if you're not using R. Except engine='R' (default), all chunks are executed in separate sessions, so the variables cannot be directly shared. So yes you can write a python snippet, but good luck trying to write a notebook.

dahart 9y ago

> org-babel capabilities blows Jupyter out of the water ... Besides all this, it's just a plain text format This feels like the argument against Slack in favor of IRC. I don't doubt it's true for you that org-babel is better, but there isn't really even that much comparison between Jupyter and org-babel, they are very different things. One of the more compelling reasons to use Jupyter is inline images and plots. Another one of the more compelling reasons to use it is it basically comes bundled with everything you need, python with it's own virtual environment that doesn't modify your system python, and a bunch of amazing libraries, numpy, scipy, matplotlib. Not needing to know emacs helps too, but that's really low on the list. > Jupyter uses a rather obtuse js on format which is not practical to work on directly. This is a wierd thing to say. Jupyter has download as .py right in the file menu. Not to mention download as Markdown, HTML, LaTeX or PDF, if you want to present or share instead of export the python.

tincholio 9y ago
> One of the more compelling reasons to use Jupyter is inline images and plots You can do those in org, since forever. I meant that the files themselves are plain text, which is good for sharing, version control, etc. ipynb files embed images with Base64 encoding, which makes seeing diffs a major PITA. >This is a wierd thing to say. Jupyter has download as .py right in the file menu. Not to mention download as Markdown, HTML, LaTeX or PDF, if you want to present or share instead of export the python. You can export org to those formats and more, but the main part is that you can organize your code (e.g, tangling to different files, etc.), and use other languages than python (or whatever other kernel you're running in Jupyter). Plus, you get to use a proper text editor instead of editing on a browser textarea.
- dahart 9y ago
  I Agree with all those points. I've used org mode for a few things, but not for python notebooks. I remember seeing a great video a few years back on using python in org mode to make a research notebook. It really made me want to try org mode for literate / notebook style programming. I think it was this one: https://youtu.be/1-dUkyn_fZA https://youtu.be/1-dUkyn_fZA It sounds like org mode does not store images inline, since you don't like the b64 images in Jupyter? I imagine that could go both ways depending on what you want. Even for diffing, you might like to see that the image changed (though I generally agree that diffing images is not ideal). If you have to package images separately when sharing, then wouldn't inline images score a point for easier sharing? > use other languages that python Agreed, and that is powerful, but this also goes to my point. Jupyter is made for python and org mode isn't. Jupyter comes with python and libraries, where with Emacs you're on your own to figure out how to install and use different languages, and setup your environment so Emacs can see them. You're on your own to bring in images and plots, where Jupyter already understands commands that output images. > Plus, you get to use a proper text editor instead of editing on a browser textarea. Yes, but the editor is Emacs. :) For a lot of people the browser textarea is a bonus because it's the same thing you use everywhere. It's uncomplicated and non-technical and utterly consistent, even if lacking any power.

todd8 9y ago

I share your opinion about the superiority of org-mode as a means to assemble a document out of various pieces. It's not hard to show nicely formatted code, the code's output, the math behind the code and perhaps a graph of the results all in a LaTeX/PDF document and or HTML. All of this can be done with a flat text file that is easy to save as a part of a project under source control. What I wonder is why are Jupyter notebooks so popular? I've tried them, but perhaps I don't understand the workflow in the way people use them. Are they intended to be works in progress where one explores ideas and looks at results? This is how I've usually used them and Mathematica's notebooks as well. For me though, my Jupyter or Mathematica notebooks end up with lots of false steps and dead-ends. To prepare a presentable form of the results I have to go back and edit the notebook to such a degree that it doesn't feel like working in a notebook as much as it is working in a complex document with a really weak set of editing tools. To be fair, I haven't used Jupyter or Mathematica for a couple of years and things may have changed. Maybe HN readers can help be understand how to more effectively use these tools.

tincholio 9y ago
> What I wonder is why are Jupyter notebooks so popular? I often wonder the same. I'm now kinda forced to use them, since they're the tool of choice in my team, but it's a major pain. I think that they're "easy" (in the way Rich Hickey describes "easy" vs "simple") to get started with (just as python, btw), but their lack of flexibility comes back to bite you sooner or later. For me, I've resorted to using a mix of EIN and ob-ipython, and then copy/pasting as needed to keep the stuff in synch with Jupyter. I'm now considering writing a simple ox-jupyter exporter, and maybe some import functionality, to avoid dealing with Jupyter directly. John Kitchin has written a basic exporter (http://kitchingroup.cheme.cmu.edu/blog/2017/01/21/Exporting-org-mode-to-Jupyter-notebooks/ http://kitchingroup.cheme.cmu.edu/blog/2017/01/21/Exporting-...), but it doesn't support inline images (it should be simple to fix this), and it doesn't really adhere to the ox- style of exports, so I think I'll probably do my own instead of adapting his (it'll be a good learning experience, for sure).
dahart 9y ago
> What I wonder is why are Jupyter notebooks so popular? How easy is it to share a Jupyter notebook with someone else, versus sharing an org-mode notebook? Think about the recipients rather than how hard it is for you. Assume the person you share with needs to be able to re-run your notebook. Assume the person you share with isn't using the same operating system that you are. Be honest and think about all the steps involved. With Jupyter, I send a single install link to Anaconda. With Emacs + org mode + python + numpy + scipy + matplotlib, I might not even know where to begin if the recipient is using Windows or Mac. The recipient needs to install emacs, and they need to know how to use Emacs. They have to know how to install python packages (and possibly a package manager), and ideally be able to use virtualenv too. If I need different libraries than what Anaconda comes with, I can put the commands in the notebook, and I won't mess up the recipient's system version of Python. With org-mode, they'd need to figure it out on their own. If I choose to use a different language than Python in my org-node notebook, the recipient will have to install that programming language and environment themselves before they can use your notebook. It's the simplicity and bundling of dependencies that make Jupyter popular. All the flexibility and power you get with org mode comes at a high price.